In earlier work, we developed a two-dimensional method for the display of DNA restriction fragments generated by the sequential action of two or more restriction enzymes. The method was found to yield new information about certain sequences repeated many times in the mammalian genome. This two-dimensional analysis of DNA has been extended by the use of cloned probes. Cloned DNA sequences coding for "30 S" RNA were studied. These DNA sequences are homologous to the DNA of Harvey rat sarcoma virus. The degree of repetition of these sequences was found to be significantly greater than the 30-fold expected. The high copy number made further analysis difficult. The technique was applied to a study of the DNA of the slime mold Physarum polycephalum. Electrophoretic characterization of DNA prepared from this organism revealed the presence of a co-purifying contaminant, and permitted the identification of the impurity as an acidic polysaccharide. These observations formed the basis of a methodology for preparing DNA free of the contaminant. The purified DNA was readily cleaved with restriction enzymes, and contained many repeated sequences.